Implementing Distributed Systems Using Linear Naming

Linear graph reduction is a simple computational model in which the cost of naming things is explicitly represented. The key idea is the notion of "linearity". A name is linear if it is only used once, so with linear naming you cannot create more than one outstanding reference to an entity. As a result, linear naming is cheap to support and easy to reason about. Programs can be translated into the linear graph reduction model such that linear names in the program are implemented directly as linear names in the model. Nonlinear names are supported by constructing them out of linear names. The translation thus exposes those places where the program uses names in expensive, nonlinear ways. Two applications demonstrate the utility of using linear graph reduction: First, in the area of distributed computing, linear naming makes it easy to support cheap cross-network references and highly portable data structures, Linear naming also facilitates demand driven migration of tasks and data around the network without requiring explicit guidance from the programmer. Second, linear graph reduction reveals a new characterization of the phenomenon of state. Systems in which state appears are those which depend on certain -global- system properties. State is not a localizable phenomenon, which suggests that our usual object oriented metaphor for state is flawed.

Preconditioning and iterative solution of symmetric indefinite linear systems arising from interior point methods for linear programming

We study the preconditioning of symmetric indefinite linear systems of equations that arise in interior point solution of linear optimization problems. The preconditioning method that we study exploits the block structure of the augmented matrix to design a similar block structure preconditioner to improve the spectral properties of the resulting preconditioned matrix so as to improve the convergence rate of the iterative solution of the system. We also propose a two-phase algorithm that takes advantage of the spectral properties of the transformed matrix to solve for the Newton directions in the interior-point method. Numerical experiments have been performed on some LP test problems in the NETLIB suite to demonstrate the potential of the preconditioning method discussed.

Automatic Analysis and Synthesis of Controllers for Dynamical Systems Based On P

I present a novel design methodology for the synthesis of automatic controllers, together with a computational environment---the Control Engineer's Workbench---integrating a suite of programs that automatically analyze and design controllers for high-performance, global control of nonlinear systems. This work demonstrates that difficult control synthesis tasks can be automated, using programs that actively exploit and efficiently represent knowledge of nonlinear dynamics and phase space and effectively use the representation to guide and perform the control design. The Control Engineer's Workbench combines powerful numerical and symbolic computations with artificial intelligence reasoning techniques. As a demonstration, the Workbench automatically designed a high-quality maglev controller that outperforms a previous linear design by a factor of 20.

Generating Communications Systems Through Shared Context

In a distributed model of intelligence, peer components need to communicate with one another. I present a system which enables two agents connected by a thick twisted bundle of wires to bootstrap a simple communication system from observations of a shared environment. The agents learn a large vocabulary of symbols, as well as inflections on those symbols which allow thematic role-frames to be transmitted. Language acquisition time is rapid and linear in the number of symbols and inflections. The final communication system is robust and performance degrades gradually in the face of problems.

Understanding Subsystems in Biology through Dimensionality Reduction, Graph Partitioning and Analytical Modeling

Biological systems exhibit rich and complex behavior through the orchestrated interplay of a large array of components. It is hypothesized that separable subsystems with some degree of functional autonomy exist; deciphering their independent behavior and functionality would greatly facilitate understanding the system as a whole. Discovering and analyzing such subsystems are hence pivotal problems in the quest to gain a quantitative understanding of complex biological systems. In this work, using approaches from machine learning, physics and graph theory, methods for the identification and analysis of such subsystems were developed. A novel methodology, based on a recent machine learning algorithm known as non-negative matrix factorization (NMF), was developed to discover such subsystems in a set of large-scale gene expression data. This set of subsystems was then used to predict functional relationships between genes, and this approach was shown to score significantly higher than conventional methods when benchmarking them against existing databases. Moreover, a mathematical treatment was developed to treat simple network subsystems based only on their topology (independent of particular parameter values). Application to a problem of experimental interest demonstrated the need for extentions to the conventional model to fully explain the experimental data. Finally, the notion of a subsystem was evaluated from a topological perspective. A number of different protein networks were examined to analyze their topological properties with respect to separability, seeking to find separable subsystems. These networks were shown to exhibit separability in a nonintuitive fashion, while the separable subsystems were of strong biological significance. It was demonstrated that the separability property found was not due to incomplete or biased data, but is likely to reflect biological structure.

An Interpolative Analytical Cache Model with Application to Performance-Power Design Space Exploration

Caches are known to consume up to half of all system power in embedded processors. Co-optimizing performance and power of the cache subsystems is therefore an important step in the design of embedded systems, especially those employing application specific instruction processors. In this project, we propose an analytical cache model that succinctly captures the miss performance of an application over the entire cache parameter space. Unlike exhaustive trace driven simulation, our model requires that the program be simulated once so that a few key characteristics can be obtained. Using these application-dependent characteristics, the model can span the entire cache parameter space consisting of cache sizes, associativity and cache block sizes. In our unified model, we are able to cater for direct-mapped, set and fully associative instruction, data and unified caches. Validation against full trace-driven simulations shows that our model has a high degree of fidelity. Finally, we show how the model can be coupled with a power model for caches such that one can very quickly decide on pareto-optimal performance-power design points for rapid design space exploration.

Certified Rapid Solution of Parametrized Linear Elliptic Equations: Application to Parameter Estimation

We present a technique for the rapid and reliable evaluation of linear-functional output of elliptic partial differential equations with affine parameter dependence. The essential components are (i) rapidly uniformly convergent reduced-basis approximations — Galerkin projection onto a space WN spanned by solutions of the governing partial differential equation at N (optimally) selected points in parameter space; (ii) a posteriori error estimation — relaxations of the residual equation that provide inexpensive yet sharp and rigorous bounds for the error in the outputs; and (iii) offline/online computational procedures — stratagems that exploit affine parameter dependence to de-couple the generation and projection stages of the approximation process. The operation count for the online stage — in which, given a new parameter value, we calculate the output and associated error bound — depends only on N (typically small) and the parametric complexity of the problem. The method is thus ideally suited to the many-query and real-time contexts. In this paper, based on the technique we develop a robust inverse computational method for very fast solution of inverse problems characterized by parametrized partial differential equations. The essential ideas are in three-fold: first, we apply the technique to the forward problem for the rapid certified evaluation of PDE input-output relations and associated rigorous error bounds; second, we incorporate the reduced-basis approximation and error bounds into the inverse problem formulation; and third, rather than regularize the goodness-of-fit objective, we may instead identify all (or almost all, in the probabilistic sense) system configurations consistent with the available experimental data — well-posedness is reflected in a bounded "possibility region" that furthermore shrinks as the experimental error is decreased.

Non-linear mechanical behavior of the elastomer polydimethylsiloxane (PDMS) used in the manufacture of microfluidic devices

Polydimethylsiloxane (PDMS) is the elastomer of choice to create a variety of microfluidic devices by soft lithography techniques (eg., [1], [2], [3], [4]). Accurate and reliable design, manufacture, and operation of microfluidic devices made from PDMS, require a detailed characterization of the deformation and failure behavior of the material. This paper discusses progress in a recently-initiated research project towards this goal. We have conducted large-deformation tension and compression experiments on traditional macroscale specimens, as well as microscale tension experiments on thin-film (≈ 50µm thickness) specimens of PDMS with varying ratios of monomer:curing agent (5:1, 10:1, 20:1). We find that the stress-stretch response of these materials shows significant variability, even for nominally identically prepared specimens. A non-linear, large-deformation rubber-elasticity model [5], [6] is applied to represent the behavior of PDMS. The constitutive model has been implemented in a finite-element program [7] to aid the design of microfluidic devices made from this material. As a first attempt towards the goal of estimating the non-linear material parameters for PDMS from indentation experiments, we have conducted micro-indentation experiments using a spherical indenter-tip, and carried out corresponding numerical simulations to verify how well the numerically-predicted P(load-h(depth of indentation) curves compare with the corresponding experimental measurements. The results are encouraging, and show the possibility of estimating the material parameters for PDMS from relatively simple micro-indentation experiments, and corresponding numerical simulations.